No, there is no penalty.
Pickpocketing in IWD is an all-or-nothing proposition. If you are successful, nothing happens other than your acquisition of someone else's property. If you fail, everyone in town attacks you.
Do you use the spell Friends (lvl 1 mage spell, adds 5 points to Cha)? If you've used it before while buying, that 5 point difference could well account for the higher prices you see now. If you have used a paladin to speak to shopkeepers, it also may have a higher Cha than your bard.